Pipes or cables which are able to be placed within the same block are invisible and cannot be removed,
whenever a server crashes without saving the placed block.

Placing blocks of the same pipe cable behavious works however. Any other full block doesn't.

That's a ghost pipe you can remove by changing enableDebugCommands = false to true in the MI config then using the debug command /mi pipes <pos> clear where <pos> is the position of the pipe in the world. This requires cheats to be enabled.